Biases of tree-independent-character-subsampling methods

Biases of tree-independent-character-subsampling methods Molecular Phylogenetics and Evolution 100 (2016) 424–443 Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev a,⇑ b Mark P. Simmons , John Gatesy Department of Biology, Colorado State University, Fort Collins, CO 80523, USA Department of Biology, University of California, Riverside, CA 92521, USA ar ti c l e i nf o ab stra ct Article history: Observed Variability (OV) and Tree Independent Generation of Evolutionary Rates (TIGER) are quick and Received 9 December 2015 easy-to-apply tree-independent methods that have been proposed to provide unbiased estimates of each Revised 16 March 2016 character’s rate of evolution and serve as the basis for excluding rapidly evolving characters. Both meth- Accepted 15 April 2016 ods have been applied to multiple phylogenomic datasets, and in many cases the authors considered their Available online 19 April 2016 trees inferred from the OV- and TIGER-delimited sub-matrices to be better estimates of the phylogeny than their trees based on all characters. In this study we use four sets of simulations and an empirical Keywords: phylogenomic example to demonstrate that both methods share a systematic bias against characters Character subsampling with more symmetric distributions of character states, against characters with greater observed http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Molecular Phylogenetics and Evolution Elsevier

Biases of tree-independent-character-subsampling methods

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Publisher
Elsevier
Copyright
Copyright © 2016 Elsevier Inc.
ISSN
1055-7903
eISSN
1095-9513
D.O.I.
10.1016/j.ympev.2016.04.022
Publisher site
See Article on Publisher Site

Abstract

Molecular Phylogenetics and Evolution 100 (2016) 424–443 Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev a,⇑ b Mark P. Simmons , John Gatesy Department of Biology, Colorado State University, Fort Collins, CO 80523, USA Department of Biology, University of California, Riverside, CA 92521, USA ar ti c l e i nf o ab stra ct Article history: Observed Variability (OV) and Tree Independent Generation of Evolutionary Rates (TIGER) are quick and Received 9 December 2015 easy-to-apply tree-independent methods that have been proposed to provide unbiased estimates of each Revised 16 March 2016 character’s rate of evolution and serve as the basis for excluding rapidly evolving characters. Both meth- Accepted 15 April 2016 ods have been applied to multiple phylogenomic datasets, and in many cases the authors considered their Available online 19 April 2016 trees inferred from the OV- and TIGER-delimited sub-matrices to be better estimates of the phylogeny than their trees based on all characters. In this study we use four sets of simulations and an empirical Keywords: phylogenomic example to demonstrate that both methods share a systematic bias against characters Character subsampling with more symmetric distributions of character states, against characters with greater observed

Journal

Molecular Phylogenetics and EvolutionElsevier

Published: Jul 1, 2016

References

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